This isn't exactly a general Linux help forum, but it's been pretty slow lately so...
For your fifth question, you might need to manually enter in the path to what you want to run, such as /usr/local/bin/some_application. Many distributions do not set up the root users' $PATH the same way as those of normal users.
What are you trying to run in superuser mode? It's best to avoid using superuser privileges whenever possible since it leaves your system vulnerable to malicious code that might try to plant trojans or otherwise modify with important files.
For question #6, I like to manually edit my ~/.xinitrc file. Desktop manager startup scripts are usually found in /etc/X11/Sessions, so if you put a line in ~/.xinitrc that contains /etc/X11/Sessions/wmaker, it should start Windowmaker (wmaker). However, your distribution probably uses something like KDM or GDM to allow you to choose between desktops graphically. They usually have a drop-down menu that you select a desktop from before logging in. If you log out, you should be able to access this menu.
Do you have any questions specific to nVidia hardware?
"Floating in a dream-like state, I am the emporer of a parallel universe." --Arch Enemy
My xorg.conf file